\section{/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFinput/NFinput.hh File Reference}
\label{NFinput_8hh}\index{/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFinput/NFinput.hh@{/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFinput/NFinput.hh}}


{\tt \#include $<$iostream$>$}\par
{\tt \#include $<$map$>$}\par
{\tt \#include $<$stdio.h$>$}\par
{\tt \#include $<$exception$>$}\par
{\tt \#include \char`\"{}../NFcore/NFcore.hh\char`\"{}}\par
{\tt \#include \char`\"{}../NFoutput/NFoutput.hh\char`\"{}}\par
{\tt \#include \char`\"{}../NFfunction/NFfunction.hh\char`\"{}}\par
{\tt \#include \char`\"{}../NFreactions/reactions/reaction.hh\char`\"{}}\par
{\tt \#include \char`\"{}TinyXML/tinyxml.h\char`\"{}}\par
\subsection*{Namespaces}
\begin{CompactItemize}
\item 
namespace {\bf NFinput}
\end{CompactItemize}
\subsection*{Classes}
\begin{CompactItemize}
\item 
class {\bf NFinput::component}
\begin{CompactList}\small\item\em Maintains information about a \doxyref{component}{p.}{classNFinput_1_1component} of a TemplateMolecule. \item\end{CompactList}\end{CompactItemize}
\subsection*{Functions}
\begin{CompactItemize}
\item 
{\bf System} $\ast$ {\bf NFinput::initializeFromXML} (string filename, bool verbose)
\begin{CompactList}\small\item\em Maintains information about a \doxyref{component}{p.}{classNFinput_1_1component} of a TemplateMolecule. \item\end{CompactList}\item 
bool {\bf NFinput::initParameters} ({\bf TiXmlElement} $\ast$pListOfParameters, map$<$ string, double $>$ \&parameter, bool verbose)
\begin{CompactList}\small\item\em Reads the parameter XML block and puts them in the parameter map. \item\end{CompactList}\item 
bool {\bf NFinput::initGlobalFunctions} ({\bf TiXmlElement} $\ast$pListOfFunctions, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, bool verbose)
\begin{CompactList}\small\item\em Reads the Function XML block and adds the Functions to the system. \item\end{CompactList}\item 
bool {\bf NFinput::initMoleculeTypes} ({\bf TiXmlElement} $\ast$pListOfMoleculeTypes, {\bf System} $\ast$system, map$<$ string, int $>$ \&allowedStates, bool verbose)
\begin{CompactList}\small\item\em Reads the MoleculeType XML block and adds the MoleculeTypes to the system. \item\end{CompactList}\item 
bool {\bf NFinput::FindReactionRuleSymmetry} ({\bf TiXmlElement} $\ast$pRxnRule, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, map$<$ string, {\bf component} $>$ \&symComps, map$<$ string, {\bf component} $>$ \&symRxnCenter, bool verbose)
\item 
bool {\bf NFinput::readPatternForSymmetry} ({\bf TiXmlElement} $\ast$pListOfMol, {\bf System} $\ast$s, string patternName, map$<$ string, {\bf component} $>$ \&comps, map$<$ string, {\bf component} $>$ \&symComps, bool verbose)
\item 
bool {\bf NFinput::generateRxnPermutations} (vector$<$ map$<$ string, {\bf component} $>$ $>$ \&permutations, map$<$ string, {\bf component} $>$ \&symComps, map$<$ string, {\bf component} $>$ \&symRxnCenter)
\item 
bool {\bf NFinput::initStartSpecies} ({\bf TiXmlElement} $\ast$pListOfSpecies, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, bool verbose)
\begin{CompactList}\small\item\em Reads a Species XML block, creates the molecules and adds them to the system. \item\end{CompactList}\item 
bool {\bf NFinput::initReactionRules} ({\bf TiXmlElement} $\ast$pListOfReactionRules, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, bool verbose)
\begin{CompactList}\small\item\em Reads a reactionRule XML block and adds the rules to the system. \item\end{CompactList}\item 
bool {\bf NFinput::initObservables} ({\bf TiXmlElement} $\ast$pListOfObservables, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, bool verbose)
\begin{CompactList}\small\item\em Reads an observable XML block and adds the new observables to the system. \item\end{CompactList}\item 
{\bf TemplateMolecule} $\ast$ {\bf NFinput::readPattern} ({\bf TiXmlElement} $\ast$pListOfMol, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, string patternName, map$<$ string, {\bf TemplateMolecule} $\ast$ $>$ \&templates, map$<$ string, {\bf component} $>$ \&comps, map$<$ string, {\bf component} $>$ \&symMap, bool verbose)
\begin{CompactList}\small\item\em Reads a pattern XML block and returns the set of new TemplateMolecule objects. \item\end{CompactList}\item 
bool {\bf NFinput::readProductPattern} ({\bf TiXmlElement} $\ast$pListOfMol, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, string patternName, vector$<$ {\bf MoleculeType} $\ast$ $>$ \&productMoleculeTypes, vector$<$ vector$<$ int $>$ $>$ \&stateInformation, vector$<$ vector$<$ int $>$ $>$ \&bindingSiteInformation, bool verbose)
\begin{CompactList}\small\item\em Reads a pattern XML block and returns the set of new TemplateMolecule objects. \item\end{CompactList}\item 
bool {\bf NFinput::parseArguments} (int argc, const char $\ast$argv[$\,$], map$<$ string, string $>$ \&argMap)
\begin{CompactList}\small\item\em Parses command line arguments from the console nicely. \item\end{CompactList}\item 
int {\bf NFinput::parseAsInt} (map$<$ string, string $>$ \&argMap, string argName, int defaultValue)
\item 
double {\bf NFinput::parseAsDouble} (map$<$ string, string $>$ \&argMap, string argName, double defaultValue)
\item 
void {\bf NFinput::parseComplexDump} (vector$<$ {\bf Outputter} $>$ \&outputter, string arg)
\item 
void {\bf NFinput::walk} ({\bf System} $\ast$s)
\item 
bool {\bf NFinput::createComplexOutputDumper} (string paramStr, {\bf System} $\ast$s, bool verbose)
\end{CompactItemize}
